Bayesian Evolutionary Analysis Sampling Trees
https://beast.community/
All issues are tracked at https://github.com/beast-dev/beast-mcmc/issues
- Added option to write doubling time in days to the log file when using a coalescent model with an exponential growth parameter.
- Added an option to write the epidemiological reproduction number (R0) to the log file when using a coalescent model with an exponential growth parameter. This requires an estimate of the mean and standard deviation of the generation time distribution to be specified in BEAUti.
- Can specify multiple HPD intervals e.g., using `--hpd 0.95,0.90,0.5'
- Can generate a KDE curve of the distribution of height values for visualisation in PearTree
- Clade MRCA heights can be calculated to avoid negative branch lengths (CA method of Heled and Bouckaert, (2013))
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Fixed TreeAnnotator not summarising 2-dimensional locations correctly — continuous phylogeographic location traits (e.g.
location1/location2) were being renamed tolocation.rate1/location.rate2in the annotated tree output. (#1242) -
Fixed performance regression in TreeAnnotator "Collecting node information" stage — processing of large tree sets became increasingly slow and eventually stalled, a regression introduced after Beta5. (#1233)
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Fixed bug in TreeAnnotator for continuous phylogeography with fixed trees — coordinate annotations were being replaced by branch lengths and then discarded when the input tree topology was fixed rather than sampled. (#1255)
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Fixed BEAUti reverting clock-rate prior to CTMC reference prior — custom rate priors (e.g. a lognormal prior on the substitution rate) specified in BEAUti were being silently replaced by the CTMC reference prior when the XML was written. (#1238)
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Fixed an issue where if the name stem was too long, the names of the log files and tree files could be truncated in the XML.
- Updated HIPSTR citation to the final published paper. (#1243)
Initial public release of BEAST X (v10.5 series).
For earlier version history see the BEAST website.